runCompareComplex           package:ScISI           R Documentation

_A _f_u_n_c_t_i_o_n _t_h_a_t _c_a_l_l_s _a_l_l _o_t_h_e_r _t_y_p_e_s _o_f _c_o_m_p_a_r_i_s_o_n _f_u_n_c_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function begins by acquiring the same vertex set for both
     BGMat1 and BGMat2. Then it calls the 'compareComplex' function to
     calculate three statistics (see 'compareComplex' man page for
     details). Next it calls calculates a similarity measure (default
     is Jaccard). Next it calls the 'runAlignment' function to greedily
     calculate an alignment between BGMat1 and BGMat2.

_U_s_a_g_e:

     runCompareComplex(BGMat1, BGMat2, index = "Jaccard", byWhich)

_A_r_g_u_m_e_n_t_s:

  BGMat1: The first bipartite graph matrix

  BGMat2: The second bipartite graph matrix

   index: The type of similarity index used

 byWhich: A parameter for the maximizeSimilarity function. It can
          either be "ROW", "COL", or "BOTH"

_V_a_l_u_e:

     The return value of runCompareComplex is a list with the following
     statistics:

  simInd: The matrix of similarity measures between two bipartite
          graphs.

maxIntersect: The output of maximizeSimilarity. A list. The first value
          is the largest similarity indices between complexes of the
          row and complexes of the columns if byWhich is "ROW" and vice
          versa if byWhich="COL". The second value returns the actual
          complex of highest similarity (column complexes if
          byWhich="ROW" and row complexes if byWhich="COL"

   equal: A list of complexes of BGMat1 equal to complexes of BGMat2.
          The values of the list are the complex, C, of BGMat1, the
          complex, K,  of BGMat2, the cardinality of C, the cardinality
          of K, and the cardinality of the intersection of C and K

  toBeRm: A character vector of complexes that should be removed if two
          bipartite graphs are merged since they would represent
          redundant complexes. If the function is called on one
          bi-partite graph, then this vector looks for redundancies
          within one database and those complexes needs to be removed
          as well.  These complexes are derived from BGMat1 only.

subcomplex: A list of complexes of BGMat1 which is contained in
          complexes of BGMat2 or vice versa. The values of the list are
          the complex, C, of BGMat1, the complex, K,  of BGMat2, the
          cardinality of C, the cardinality of K, and the cardinality
          of the intersection of C and K

toBeRmSubC: A character vector. The same as toBeRm but instead of
          redundant protein complexes, this is a compilation of all the
          sub-complexes between two bi-partite graph matrices
          (bi-partite graph matrices need not be different)

_A_u_t_h_o_r(_s):

     Tony Chiang

_E_x_a_m_p_l_e_s:

     #go = getGOInfo()
     #mips = getMipsInfo()
     #goM = createGOMatrix(go)
     #mipsM = createMipsMatrix(mips)
     #cc = runCompareComplex(mipsM, goM, byWhich = "ROW")

